.TH editconf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
editconf - edits the box and writes subgroups 

.B VERSION 4.5
.SH SYNOPSIS
\f3editconf\fP
.BI "\-f" " conf.gro "
.BI "\-n" " index.ndx "
.BI "\-o" " out.gro "
.BI "\-mead" " mead.pqr "
.BI "\-bf" " bfact.dat "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-[no]w" ""
.BI "\-[no]ndef" ""
.BI "\-bt" " enum "
.BI "\-box" " vector "
.BI "\-angles" " vector "
.BI "\-d" " real "
.BI "\-[no]c" ""
.BI "\-center" " vector "
.BI "\-aligncenter" " vector "
.BI "\-align" " vector "
.BI "\-translate" " vector "
.BI "\-rotate" " vector "
.BI "\-[no]princ" ""
.BI "\-scale" " vector "
.BI "\-density" " real "
.BI "\-[no]pbc" ""
.BI "\-[no]grasp" ""
.BI "\-rvdw" " real "
.BI "\-sig56" " real "
.BI "\-[no]vdwread" ""
.BI "\-[no]atom" ""
.BI "\-[no]legend" ""
.BI "\-label" " string "
.BI "\-[no]conect" ""
.SH DESCRIPTION
\&editconf converts generic structure format to \fB .gro\fR, \fB .g96\fR
\&or \fB .pdb\fR.
\&


\&The box can be modified with options \fB \-box\fR, \fB \-d\fR and
\&\fB \-angles\fR. Both \fB \-box\fR and \fB \-d\fR
\&will center the system in the box, unless \fB \-noc\fR is used.
\&


\&Option \fB \-bt\fR determines the box type: \fB triclinic\fR is a
\&triclinic box, \fB cubic\fR is a rectangular box with all sides equal
\&\fB dodecahedron\fR represents a rhombic dodecahedron and
\&\fB octahedron\fR is a truncated octahedron.
\&The last two are special cases of a triclinic box.
\&The length of the three box vectors of the truncated octahedron is the
\&shortest distance between two opposite hexagons.
\&The volume of a dodecahedron is 0.71 and that of a truncated octahedron
\&is 0.77 of that of a cubic box with the same periodic image distance.
\&


\&Option \fB \-box\fR requires only
\&one value for a cubic box, dodecahedron and a truncated octahedron.
\&


\&With \fB \-d\fR and a \fB triclinic\fR box the size of the system in the x, y
\&and z directions is used. With \fB \-d\fR and \fB cubic\fR,
\&\fB dodecahedron\fR or \fB octahedron\fR boxes, the dimensions are set
\&to the diameter of the system (largest distance between atoms) plus twice
\&the specified distance.
\&


\&Option \fB \-angles\fR is only meaningful with option \fB \-box\fR and
\&a triclinic box and can not be used with option \fB \-d\fR.
\&


\&When \fB \-n\fR or \fB \-ndef\fR is set, a group
\&can be selected for calculating the size and the geometric center,
\&otherwise the whole system is used.
\&


\&\fB \-rotate\fR rotates the coordinates and velocities.
\&


\&\fB \-princ\fR aligns the principal axes of the system along the
\&coordinate axes, this may allow you to decrease the box volume,
\&but beware that molecules can rotate significantly in a nanosecond.
\&


\&Scaling is applied before any of the other operations are
\&performed. Boxes and coordinates can be scaled to give a certain density (option
\&\fB \-density\fR). Note that this may be inaccurate in case a gro
\&file is given as input. A special feature of the scaling option, when the
\&factor \-1 is given in one dimension, one obtains a mirror image,
\&mirrored in one of the plains, when one uses \-1 in three dimensions
\&a point\-mirror image is obtained.


\&Groups are selected after all operations have been applied.


\&Periodicity can be removed in a crude manner.
\&It is important that the box sizes at the bottom of your input file
\&are correct when the periodicity is to be removed.
\&


\&When writing \fB .pdb\fR files, B\-factors can be
\&added with the \fB \-bf\fR option. B\-factors are read
\&from a file with with following format: first line states number of
\&entries in the file, next lines state an index
\&followed by a B\-factor. The B\-factors will be attached per residue
\&unless an index is larger than the number of residues or unless the
\&\fB \-atom\fR option is set. Obviously, any type of numeric data can
\&be added instead of B\-factors. \fB \-legend\fR will produce
\&a row of CA atoms with B\-factors ranging from the minimum to the
\&maximum value found, effectively making a legend for viewing.
\&


\&With the option \-mead a special pdb (pqr) file for the MEAD electrostatics
\&program (Poisson\-Boltzmann solver) can be made. A further prerequisite
\&is that the input file is a run input file.
\&The B\-factor field is then filled with the Van der Waals radius
\&of the atoms while the occupancy field will hold the charge.
\&


\&The option \-grasp is similar, but it puts the charges in the B\-factor
\&and the radius in the occupancy.
\&


\&Option \fB \-align\fR allows alignment
\&of the principal axis of a specified group against the given vector, 
\&with an optional center of rotation specified by \fB \-aligncenter\fR.
\&


\&Finally with option \fB \-label\fR editconf can add a chain identifier
\&to a pdb file, which can be useful for analysis with e.g. rasmol.
\&


\&To convert a truncated octrahedron file produced by a package which uses
\&a cubic box with the corners cut off (such as Gromos) use:

\&\fB editconf \-f in \-rotate 0 45 35.264 \-bt o \-box veclen \-o out\fR

\&where \fB veclen\fR is the size of the cubic box times sqrt(3)/2.
.SH FILES
.BI "\-f" " conf.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " out.gro" 
.B Output, Opt.
 Structure file: gro g96 pdb etc. 

.BI "\-mead" " mead.pqr" 
.B Output, Opt.
 Coordinate file for MEAD 

.BI "\-bf" " bfact.dat" 
.B Input, Opt.
 Generic data file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-[no]ndef"  "no    "
 Choose output from default index groups

.BI "\-bt"  " enum" " triclinic" 
 Box type for \-box and \-d: \fB triclinic\fR, \fB cubic\fR, \fB dodecahedron\fR or \fB octahedron\fR

.BI "\-box"  " vector" " 0 0 0" 
 Box vector lengths (a,b,c)

.BI "\-angles"  " vector" " 90 90 90" 
 Angles between the box vectors (bc,ac,ab)

.BI "\-d"  " real" " 0     " 
 Distance between the solute and the box

.BI "\-[no]c"  "no    "
 Center molecule in box (implied by \-box and \-d)

.BI "\-center"  " vector" " 0 0 0" 
 Coordinates of geometrical center

.BI "\-aligncenter"  " vector" " 0 0 0" 
 Center of rotation for alignment

.BI "\-align"  " vector" " 0 0 0" 
 Align to target vector

.BI "\-translate"  " vector" " 0 0 0" 
 Translation

.BI "\-rotate"  " vector" " 0 0 0" 
 Rotation around the X, Y and Z axes in degrees

.BI "\-[no]princ"  "no    "
 Orient molecule(s) along their principal axes

.BI "\-scale"  " vector" " 1 1 1" 
 Scaling factor

.BI "\-density"  " real" " 1000  " 
 Density (g/l) of the output box achieved by scaling

.BI "\-[no]pbc"  "no    "
 Remove the periodicity (make molecule whole again)

.BI "\-[no]grasp"  "no    "
 Store the charge of the atom in the B\-factor field and the radius of the atom in the occupancy field

.BI "\-rvdw"  " real" " 0.12  " 
 Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file

.BI "\-sig56"  " real" " 0     " 
 Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 

.BI "\-[no]vdwread"  "no    "
 Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field

.BI "\-[no]atom"  "no    "
 Force B\-factor attachment per atom

.BI "\-[no]legend"  "no    "
 Make B\-factor legend

.BI "\-label"  " string" " A" 
 Add chain label for all residues

.BI "\-[no]conect"  "no    "
 Add CONECT records to a pdb file when written. Can only be done when a topology is present

.SH KNOWN PROBLEMS
\- For complex molecules, the periodicity removal routine may break down, 

\- in that case you can use trjconv.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
